I am currently using ST2 build 2152 on linux x86_64 and I have remapped my Caps Lock key to CTRL. When I try to use shortcuts which require both keys such as Close Window (Shift+Ctrl+W), they do not work with the remapped Caps Lock key, but do correctly work with the true CTRL key. The remapped key works in every other application, so I know it's not a hardware problem.